Hi,
I'm doing protein-protein docking but the problem is one of the two proteins uses the same domain for other proteins too to interact. I want to know if a single domain interact with multiple proteins so can we use it to dock against the one protein. is it possible that it is sharing the same residue to interact with multiple proteins?
Hi there,
Indeed it is possible. For instance our works on yeast Trm112 protein is a nice illustration : this protein is necessary for activating 4 different methyltransferases and uses the same strategy for interaction with its 4 partners. For info, please read the following:
Article Insights into molecular plasticity in protein complexes from...
Article Trm112, a Protein Activator of Methyltransferases Modifying ...
Of course, if the same residues on one protein domain can interact with multiple binding partners, the different binding partners will usually compete with each other - this is often the case for neutralizing antibodies that bind a ligand and compete with the receptor or vice versa. The N-terminal domain of CD4 normally interacts with the MHC, but the same residues are recognized by HIV GP120.
Yes, of course. A very best example is the human proteins, which are targeted by viral proteins in order to hijack cell cycle. For instance, the oncoprotein E6 from high-risk Human Papilloma Virus (HPV) is interacting with the LxxLL motif present in numerous human proteins, among those the well-characterized E6AP. This complex is therafter binding to p53, leading to the p53 degradation by the proteome. In a non-infected cell, the LxxLL motif of E6AP is used to interact with other human proteins.
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